New: CloudBioLinux packages are now listed on biogems.info !

# biogem description by cite version released stars issues source build total 90d*) 7d   90d**)
downloads commits
bio
Bioinformatics library !
BioRuby project
10 months
288
12
114387
0
0
Parser of scientific names !
Dmitry Mozzherin
8 months
21
3
67876
0
0
Binder of samtools for Ruby, on the top
Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal
10 months
23
9
50139
0
10
Biogem is a software generator for Ruby in !
Raoul J.P. Bonnal, Pjotr Prins
23 months
15
12
47624
0
0
Blast search made easy! !
Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.
6 weeks
88
52
37113
0
0
Gadgets for bioinformatics
Shintaro Katayama
2 years
1
33738
0
0
The Ruby ucsc api: accessing the ucsc genome !
Hiroyuki Mishima, Jan Aerts
2 years
16
1
32102
0
0
Http requests to entrez e-utilities
Jared Ning
12 months
6
1
29971
0
0
Create pretty svg-format images of features, gene models
Dan MacLean
2 years
11
5
27510
0
0
A Ruby api for interacting with biomart services !
Darren Oakley
4 years
18
5
27390
0
0
Maf parser for BioRuby
Clayton Wheeler
3 years
10
36
23439
0
0
Gff3 parser for big data !
Pjotr Prins
3 years
6
2
22891
0
0
Very fast parallel blast xml to rdf/html/json/yaml/csv transformer !
Pjotr Prins
12 months
12
1
20976
0
0
A biogem to submit jobs on a queue
Francesco Strozzi
3 years
5
...
20633
0
0
Interfaces with biomodel search engine !
Niall Beard
4 years
1
...
20378
0
0
Log4r wrapper with extra features for roles and !
Pjotr Prins
4 years
4
2
18502
0
0
A simple obo file handler !
mjy
4 years
5
...
17517
0
0
Tool to work with polyploids, ngs and molecular
Ricardo H.  Ramirez-Gonzalez
8 months
2
1
17359
0
3
An open source framework for transforming heterogeneous data
Joachim Baran, Kevin B. Cohen, Geraint Duck et al.
16 months
12
3
16804
0
0
Swiss army knife of tabulated data; transforming/filtering tab/csv
Pjotr Prins
23 months
9
20
14846
0
0
A fast parser for fastq files
Francesco Strozzi
3 years
10
...
14365
0
0
Support for multiple sequence alignments (msa)
Pjotr Prins
23 months
8
5
14363
0
0
Data mining algorithms for jRuby
arrigonialberto86
2 years
15
3
14177
0
0
A tool to classify and manipulate pfemp1 dbl-alpha
George Githinji
3 years
12080
0
0
Low memory sequence emitters
Pjotr Prins
23 months
11
1
11609
0
0
Pipeline to remove contaminations from est libraries
Philipp Comans
4 years
2
1
11532
0
0
A wrapper for the signal peptide prediction algorith
Ben J Woodcroft
21 months
3
...
11074
0
0
A nexus file format (phylogenetic inference) parser in !
mjy
5 years
1
...
10927
0
0
Build genome output files
Michael Barton
2 years
5
...
10710
0
0
A biogem for counting small kmers for fingerprinting
Ben J Woodcroft
2 years
5
...
10257
0
0
A BioRuby plugin for interaction with the transmembrane
Ben J. Woodcroft
3 years
2
...
10072
0
0
BioRuby assembly plugin
Chase Miller, Francesco Strozzi
5 years
4
...
9903
0
0
Simple morphbank (http://morphbank.net) services accessor !
mjy
4 years
1
...
9902
0
0
Bio-ngs provides a framework for handling ngs data
Francesco Strozzi, Raoul J.P. Bonnal
3 years
30
15
9896
0
0
Ruby wrapper for sambamba tool
Artem Tarasov
3 years
2
...
9728
0
0
Fast multi-purpose multi-threaded vcf parser
Pjotr Prins
3 months
31
8
9547
0
36
Lightweight Ruby api for ncbi eutils
Joon Lee, aka seouri
2 years
8
...
9518
0
0
BioRuby plugin for reading and writing nexml (http://nexml.org) !
Rutger Vos, Anurag Priyam
3 years
8
2
9359
0
0
A BioRuby plugin for calculating the isoelectric point
George Githinji, Pascal Betz
4 years
3
...
9327
0
0
Supports linking of models within a ror application !
Stuart Owen, Quyen Nguyen
2.2
2 years
...
9121
0
0
Basespace Ruby sdk is a Ruby based software
Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.
2 years
13
2
8386
0
0
Library for visualizing genomic regions !
Jan Aerts
1.4
8 years
22
1
8336
0
0
A BioRuby plugin: handling genomic interavals and overlaps
Hiroyuki Mishima
5 years
4
...
8296
0
0
Rocker
Luis (Coto) Orellana, Luis M. Rodriguez-R
5 months
8171
0
0
Reading/writing bgzf blocks
Artem Tarasov, Clayton Wheeler
3 years
3
...
7930
0
0
Parser to work with file formats used in
Ben J Woodcroft
16 months
...
7690
0
0
Running and parsing of the protein transmembrane domain
Ben J Woodcroft
5 years
1
...
7584
0
0
Server for polymarker. to be used with cron
Ricardo H.  Ramirez-Gonzalez
14 months
...
7406
0
0
Ruby binding for bwa mapping software
Francesco Strozzi
5 years
4
...
6931
0
0
Read and manipulate cd-hit clusters
George Githinji
3 years
6886
0
0
Ruby binding for samtools tabix
throwern
2 years
5
...
6694
0
0
A plugin that allows you to parse large
robsyme
4 years
1
...
6686
0
0
Gene ontology (go) interface for Ruby
Ben J Woodcroft
5 years
10
...
6521
0
0
Iterate through a samtools pileup file
Ben J. Woodcroft
3 years
2
...
6469
0
0
Api to ensembl databases !
Jan Aerts, Francesco Strozzi
5 years
41
5
6046
0
0
Ruby wrapper for the gff3-pltools
Marjan Povolni
3 years
13
19
5712
0
0
Chembl rest api client, parser and container
Mitsuteru Nakao
3 years
1
1
5613
0
0
Next-generation mapping of mutations
Dan MacLean
3 years
2
...
5581
0
0
A general purpose framework for scripted handling of development/stable
mjy
3 years
2
1
5562
0
0
Ruby binding to the ucsc kent utilities
throwern
3 years
2
...
5559
0
0
Timeseries modules for statsample
Ankur Goel, Claudio Bustos
2 years
5360
0
0
Implementation of the plasmoap algorithm
Ben J Woodcroft
2 weeks
1
...
5349
0
0
Retrieve dna sequence from ucsc using given coordinates
Andrei Rozanski
8 months
5297
0
0
Publish scientific results to the semantic web !
Will Strinz
23 months
3
16
5199
0
0
Bioinformatics triple-store support
Pjotr Prins
3 years
4
1
5176
0
0
Geneexpression illuminahumanannotation
Raoul J.P. Bonnal
5 years
1
...
5156
0
0
Parse affymetrix cel/cdf files
Pjotr Prins
4 years
2
1
5146
0
0
This biogem is built around krona, a flashy
Ben J. Woodcroft
4 months
1
...
5048
0
0
BioRuby plugin for unichem rest web service
Mitsuteru Nakao
3 years
4779
0
0
Identifying problems with gene predictions !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
7 weeks
...
4725
0
0
Reports whether a nucleotide change results in synonymous
Dan MacLean
2 years
...
4675
0
0
BioRuby core plugins, most and stable plugins. blastxmlparser, !
Raoul J.P. Bonnal
4 years
1
...
4559
0
0
Bindings to some internals of the velvet assembler
Ben Woodcroft
16 months
1
4557
0
0
Programmatic interface to the cnls nuclear localisation signal
Ben J. Woodcroft
3 years
2
...
4381
0
0
Enables the localisation predictor wolf psort to be
Ben J Woodcroft
4 years
1
...
4362
0
0
Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)
Andrei Rozanski
2 years
1
...
4210
0
0
Parse pfam hmm definition files
Ben J. Woodcroft
3 years
1
...
3987
0
0
A protparam compatible utility for BioRuby
hryk
3 years
2
...
3919
0
0
Bio-gag is a biogem for detecting and correcting
Ben J Woodcroft
3 years
2
...
3817
0
0
Dead simple method of running shell commands from
Ben J. Woodcroft
2 weeks
...
3583
0
2
A web app wrapper for genevalidator !
Monica Dragan, Ismail Moghul, Anurag Priyam et al.
7 months
...
3391
0
0
Pass a full citation, get the bibtex back, !
Matt Yoder
18 months
1
3211
0
0
Biostars data-mining and statistical analysis
Joachim Baran
2 years
3177
0
0
Ruby parser for fastqc output
Tazro Inutano Ohta
4 weeks
2
...
3076
0
51
Enables parsing of hmmer version 3 reports
Christian Zmasek, Ben J Woodcroft
9 months
2
1
3042
0
0
Gggenome Ruby client
Mitsuteru Nakao
2 years
1
...
2872
0
0
Client for xoopit's cloudquery api
Cameron Walters, nb.io
7 years
5
...
2810
0
0
Ruby ensembl rest api
Alberto Donizetti
2 years
3
...
2807
0
0
Rubybhl is a simple request/response wrapper for the !
Matt Yoder
2 years
6
...
2807
0
0
Hello world plugin for the BioRuby (just for
Toshiaki Katayama
5 years
3
...
2702
0
0
Generalized linear models for statsample
Ankur Goel
2 years
2695
0
0
BioRuby plugin for sun grid engine
Toshiaki Katayama
5 years
4
...
2689
0
0
Digests dna based on restriction enzyme cut patterns !
Trevor Wennblom
4 years
1
2662
0
0
Does high pairwise alignment of sequencing reads with
John T. Prince
6 years
1
...
2586
0
0
Fast storage and comparison of chr+pos(+alt) locations
Pjotr Prins
7 months
2
1
2585
0
0
Interface for express beta diversity
Ben J. Woodcroft
2 years
...
2485
0
0
A method to get the nucleotide sequence of
Ben J Woodcroft
5 years
1
...
2465
0
0
Bio-repeatmasker
Andrei Rozanski
2 years
...
2427
0
0
BioRuby core ext: plugins which require external library !
Raoul J.P. Bonnal, Pjotr Prins
4 years
1
...
2407
0
0
Meta package for biolinux distribution !
Raoul J.P. Bonnal
4 years
2
...
2392
0
0
A Ruby api to the ensembl database !
Jan Aerts, Francesco Strozzi
4 years
4
...
2382
0
0
Restriction enzyme dataset !
Sir Richard J. Roberts, Trevor Wennblom
4 years
...
2375
0
0
One-line summary of your gem
Toshiaki Katayama
4 years
1
...
2357
0
0
A sequence read archive (sra) download script and
Ben J. Woodcroft
4 months
2
...
2354
0
0
Biological extensions for the intermine webservice client library
Alex Kalderimis
4 years
1
...
2344
0
0
Decoding the dbsnp bitfield
Hiroyuki Mishima
4 years
4
...
2335
0
0
Wrapper around the exportpred algorithm for predicting p
Ben J Woodcroft
4 years
1
...
2313
0
0
Phyloxml plugin for BioRuby
Diana Jaunzeikare, Clayton Wheeler
3 years
3
1
2312
0
0
Hydropathy scale for BioRuby
Ben J Woodcroft
4 years
1
...
2298
0
0
A parser for cigar format alignments
Ben J Woodcroft
2 years
4
...
2280
0
0
A simple biogem that allows computation of the
Ben J Woodcroft
4 years
1
...
2279
0
0
Web server for bio-samtools
homonecloco
23 months
...
2195
0
0
A programmatic interface to the ipcress in-silico pcr
Ben J Woodcroft
3 years
3
...
2135
0
0
Build graph with jRuby
Matteo Picciolini
3 years
2117
0
0
Helper methods for reading .delta files
robsyme
13 months
...
2041
0
0
Csshttprequest is cross-domain ajax using css as a
Cameron Walters, Randy Reddig
7 years
88
1
1954
0
0
A pipeline manager
Francesco Strozzi, Raoul Jean Pierre Bonnal
6 days
12
7
1924
0
0
Reads metadata from integrated microbial genomes (img) metadata
Ben J. Woodcroft
3 years
...
1852
0
0
Parse stockholm sequence alignment format
Ben J. Woodcroft
2 years
2
...
1664
0
0
Ruby wrapper to run standard-raxml for maximum likelihood
Fernando Izquierdo
2 years
...
1584
0
0
Fast download blast databases from ncbi beta
Anurag Priyam
10 weeks
2
...
1497
0
0
Aggregate fastqc (quality control for next generation sequencing
Raoul Jean Pierre Bonnal
10 months
...
1334
0
0
The api for freebayes version #{bio::freebayes::extversion}
Natapol Pornputtapong
11 months
1287
0
0
Mine publications for gene names
Pjotr Prins
2 years
...
1219
0
0
Ruby inferface for kseq.h by heng li for
Fedor Gusev
21 months
1
...
1130
0
0
A restful service for sharing genomic data !
Joachim Baran, Robert Buels, Michel Dumontier
2 years
1111
0
0
A Ruby wrapper on the open tree api beta
Matt Yoder
19 months
1
...
1082
0
0
Tools to work with fasta files, indexed with
homonecloco
19 months
...
1029
0
0
Tools to manipulate blat files from the command
homonecloco
19 months
...
1006
0
0
Faldo location output method for bio::location in BioRuby
Joachim Baran, Naohisa Goto
18 months
...
975
0
0
Emulates as if old BioRuby biofetch alives
Naohisa Goto
17 months
...
970
0
0
Api of picard tool
Natapol Pornputtapong
11 months
885
0
0
Csshttprequest is cross-domain ajax using css disabled
Cameron Walters, Randy Reddig
0.1
7 years
866
0
0
A pipeline creator for BioRuby
Natapol Pornputtapong
8 months
594
0
0
Tools for jaspar motifs in BioRuby
Jessica Lee, Wasserman Lab
7 months
...
574
0
0
Basic wrapper for the kallistio mapper
homonecloco
7 months
1
...
557
0
0
Methods for handling multiwell plate annotations
Steve Pettitt
3 months
...
394
0
0
A Ruby wrapper for bio sparql service
Natapol Pornputtapong
12 months
374
0
0
Parsing and mutation calling from sam, cigar and
Stephen Pettitt
2 months
...
334
0
0
pre
pre
...
0
0
0
*) gem downloads (total & last 90 days) from rubygems.org as of 2016-05-03
**) number of commits on GitHub (last 7 days & last 90 days)